Research workbench
Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase D273N mutant complexed with N-acetyl phosphonamidate-D-glucosamine-6- phosphate
Analyse Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase D273N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P53
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-6-phosphate deacetylase
- EC
- 3.5.1.25
- UniProt
- P0AF18
- Ligands
- NNG, ZN
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) | protein | 382 | 31% helix, 29% strand | P0AF18 |
Ligands and binding sites
- NNG · 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-6-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.59 | 0.82 | 32 | ZN, NNG |
| 2 | 157 | 0.58 | 0.83 | 31 | ZN, NNG |
Interfaces
1 interface between chains.
- A–B · 1012 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2P53 · Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase D273N mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AF18 · AlphaFold monomer V2.0 prediction for N-acetylglucosamine-6-phosphate deacetylase (P0AF18) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0AF18
- Elsewhere: RCSB PDB 2P53 · PDBe 2P53 · UniProt P0AF18
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